ACNUC

Sequence retrieval system for the nucleotide (GenBank, EMBL) and protein (UniProt) sequence databases and for many other systems following the same formats. Full description available froim the software home page.

Aureme

The toolbox AuReMe allows for the Automatic Reconstruction of Metabolic networks based on the combination
of multiple heteregeneous data and knowledge sources. Since 2016, the workflow has been made available
as a Docker image to facilitate its distribution among the scientific community

Autograph

AutoGRAPH is an integrated web server for multi-species comparative genomic analysis. It is designed for constructing and visualizing synteny maps between two or three species, determination and display of macrosynteny and microsynteny relationships among species, and for highlighting evolutionary breakpoints.

BCSearch

BCSearch is a fast and flexible approach to identify linear fragments similar to a query in large collections of structures. It addresses two basic questions:
Among a subset of structures, what sequences are compatible with the conformation of my query ?
Are there conformations similar to my query in other proteins ? Is it observed elsewhere ?
BCSearch is based on a new similarity approach, based on a Binet Cauchy (BC) kernel. The approach measures the correlation between the volumes of all the tetraedron of the query and that of a target. The similarity (BCscore) is scored between -1 and 1, where a value of 1 corresponds to the exact same conformation than the query, and -1 to the mirror conformation. Values close to 0 correspond to unrelated fragments. The BCscore is more stringent than other criteria such as the alpha carbon RMS deviation. Particularly, fragments with partly dissimilar shapes are poorly scored and consequently collections of matches are usually less noisy, which makes them better suited for the analysis of the local structure-sequence relationship. In addition, since no superimposition is required, the similarity search is very fast, making possible to mine large collections of structures.

BioMAJ

BioMAJ (BIOlogie Mise A Jour) is a workflow engine dedicated to data synchronization and processing.
The software automates the update cycle and the supervision of the locally mirrored databank repository.
The software is free and released under AGPL v3 based licence.

BioMAJ2Galaxy

BioMAJ2Galaxy makes it possible to configure BioMAJ to automatically download some reference data, to then convert them and/or index it in various formats, and then make this data available in a Galaxy server using data libraries or data managers.

BioShaDock

BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts deﬁned in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user deﬁned tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists.

CesGO

CeSGO offers a complete Virtual Research Environment (VRE) for Life Sciences. This VRE is based on a collaborative environment built on Wordpress and BuddyPress. It associated to the data sharing services of Owncloud and the SEEK platform.
Main site : https://www.cesgo.org/en/
Collaborative platform : https://www.cesgo.org/collaboration
Data management platform : https://data-access.cesgo.org
Scientific data platform : https://seek.cesgo.org/

fpocket

fpocket is a very fast, open source protein pocket (cavity) detection algorithm based on Voronoi tessellation. It was developed in the C programming language and is currently available as command line driven program, and from now as a web server too.

Frog2

Frog is intended to generate 3D for drugs, usually described using a 1D or 2D representation. Frog performs isomer identification from ambiguous compound description. Frog is able to generate multi-conformations per isomer.

GalaxEast

The objective of GalaxEast (http://www.galaxeast.fr) is to provide a reliable public Galaxy instance, with guaranteed availability and accessibility. GalaxEast offers a catalogue of about a hundred tools, mainly for handling of sequencing data (ChIP-seq, RNA-seq and DNAseq) high speed. The addition of proteomic and spectroscopy data analysis tools is planned for 2014. The tools come from both the official Galaxy toolshed and the developments of bioinformaticians from the local community. The new tools will be made available in the platform toolshed. The platform has a wiki that allows users to find documentation and request the addition of new tools and genomes.

Galaxy (piloté par Sigenae)

Galaxy is a workbench available for biologists from Sigenae Platform. Galaxy objectives are:
Make bioinfo Linux tools accessible to biogists.
Hide the complexity of the infrastructure.
Allow creation, execution and sharing of workflows.

Galaxy-LD

Galaxy-LD is a tool dedicated to the generation of provenance graphs (RDF, PROV-O ontology) based on Galaxy user histories. The tool is currently available through a command line interface. A web-based user interface is under active development.

GATB

The Genome Analysis Toolbox with de-Bruijn graph (GATB) provides a set of highly efficient algorithms to analyse NGS datasets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes).

GO-Docker

It is a cluster management tool using Docker as execution/isolation system. The software does not manage however itself the dispatch of the commands on the remote nodes. For this, it integrates with container management tools (Docker Swarm, Apache Mesos, ...)

HHalign-Kbest

HHalign-Kbest is useful to automatically obtain optimized alignments and models in case of low sequence identity (<35%) between a query and a template protein. It can generate k suboptimal (e.g. top-k scoring) alignments rather than only the optimal one which may contain small to large errors.

IntegronFinder

IntegronFinder is a program that detects integrons in DNA sequences. The program is available on a webserver (galaxy), or by command line (IntegronFinder on github).
Integrons are major genetic element, notorious for their major implication in the spread of antibiotic resistance genes. More generally, integrons are gene-capturing device, whose broader evolutionary role remains poorly understood. IntegronFinder is able to detect with high accuracy integron in DNA sequences. It is accurate because it combines the use of HMM profiles for the detection of the essential protein, the site-specific integron integrase, and the use of Covariance Models for the detection of the recombination site, the attC site.
IntegronFinder can also annotate gene cassettes (CDS nearby attC sites) using Resfams, a database of HMM profiles aiming at annotating antibiotic resistance genes. This database is provided but the user can add any other HMM profiles database of its own interest.

InterEvDock

InterEvDock is a server for protein docking running the InterEvScore potential specifically designed to integrate evolutionary information in the docking process. The InterEvScore potential was developed for heteromeric protein interfaces and combines a residue-based multi-body statistical potential with evolutionary information derived from the multiple sequence alignments of each partner in the complex.

MEMHDX

MEMHDX allows users to perfom an automated workflow to analyze, validate and visualize large HDX-MS datasets. The input file is the output of DynamX software from Waters. Output files provide a plot of the data, the fitted model for each peptide, a plot of the calculated p -values, and a global visualization of the experiment. User could also obtain an overview of all peptides on the 3D structure.
ref:
Véronique Hourdel, Stevenn Volant, Darragh P. O’Brien, Alexandre Chenal, Julia Chamot-Rooke, Marie-Agnès Dillies, Sébastien Brier; MEMHDX: an interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets. Bioinformatics 2016; 32 (22): 3413-3419. doi: 10.1093/bioinformatics/btw420

Minia

Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet).

Mobyle

Mobyle is a framework and web portal specifically aimed at the integration of bioinformatics software and databanks.
Mobyle is the successor of Pise and the RPBS server, previous systems that provided web environments to define and execute bioinformatics analyses.
Functionalities:
data reusability: the tagging of the user data facilitates the reuse of input values or results between different programs.
automatic data validation and format conversion: the description of the expected data and their format allows to verify and convert input values if necessary.
service discovery and workflow authoring assistance: services are provided through a searchable menu; furthermore, type compatibility mechanisms between results and potential program inputs let users either interactively pipe tasks or build complete workflows before to run them.
Based on extensive user studies, we developed the end-user interface as a Web Portal that provides a global and integrated view of all the elements needed to perform analyses, such as the available programs, the submitted jobs and the data of interest.
References:
Bertrand Néron, Hervé Ménager, Corinne Maufrais, Nicolas Joly, Julien Maupetit, Sébastien Letort, Sébastien Carrere, Pierre Tuffery, and Catherine Letondal
Mobyle: a new full web bioinformatics framework
Bioinformatics (2009); 25 (22): 3005-3011. doi:10.1093/bioinformatics/btp493.

NG6

The platform works in tight collaboration with the GeT sequencing platform for the management and the analysis of data produced by their Roche 454 and Illumina HiSeq sequencers.
NG6 is an extensible sequencing provider oriented LIMS. It includes read quality control and first level analysis processes which ease the data validation made jointly by the sequencing facility staff ant the end-users. It provides a secured user-friendly interface to visualize and download the raw sequences files and the analysis results.

2
Associated keyword(s)

Interfaces, web portals

Data management and transfer

Conditions of use

The NG6 code is freely available on the mulcyber forge. To ease the installation, the package and all its dependencies are also available as a virtual machine. Installing and maintaining the system would require expertise in Linux system administration.
Available by the web site for users

ORDO

Orphanet Rare Disease Ontology: Nomenclature, classifications and scientific data on rare diseases exploitable in an ontological form in OWL format. Elaborated in partnership with the European Bioinformatics Institute (EBI ; Contact Helen Parkinson). Available since January 2014.

PEP-FOLD

PEP-FOLD is a de novo approach aimed at predicting peptide structures from amino acid sequences.
This method, based on structural alphabet SA letters to describe the conformations of four consecutive residues, couples the predicted series of SA letters to a greedy algorithm and a coarse-grained force field.

PepPSY

PepPSy has been developed as a user-friendly gene expression-based prioritization system, to help investigators to determine in which human tissues they should look for an unseen protein and curators to quickly look at available transcriptomics/proteomics data for a list of proteins.

Protomata

Given a sample of (unaligned) sequences belonging to a structural or functional family of proteins, Protomata-Learner infers automata characterizing the family. Automata are graphical models representing a (potentially infinite) set of sequences.

ReproGenomics Viewer

The ReproGenomics Viewer (RGV) is a cross-species genomic toolbox for the reproductive community. The system is based on the implementation of a JBrowse genome browser and a Galaxy bioinformatics workflow environment.
Mis en place en 2015

RNAbrowse nouvelle version

55 instances including 18 Sigenae.
Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quiet diverse. RNAbrowse is an user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data.

6
Associated keyword(s)

NGS data analysis

Transcriptomics (RNA-seq)

Differential gene expression analysis

Transcripts and transcript variants analysis

Variant calling

Interfaces, web portals

Conditions of use

The software package is available under the GNU General Public License (GPL) and can be downloaded from the mulcyber forge.
Available on web sites for users.

RNAspace

RNAspace is a platform which aims at providing an integrated environment for non-coding RNA annotation.
The increasing number of ncRNA discovered since 2000 and the lack of user friendly tools for finding and annotating them, have made necessary to propose to biologists an in silico environment allowing structural and functional annotations of these molecules with regard to available protein genes annotation environments.
RNAspace makes available a variety of ncRNA gene finders and ncRNA databases as well as user-friendly tools to explore computed results including comparison, visualization and edition of putative RNAs. RNAspace also allows to export putative RNAs in various formats.

3
Associated keyword(s)

Analysis of gene expression regulation

Small and long non-coding RNAs

Sequence annotation

Conditions of use

RNAspace is an open source project. It is developed in Python. It is copyrighted with the GNU General Public License, and is free (in the GNU sense) for all to use, and is in constant development. RNAspace is hosted at Sourceforge. It is also available as a web server at rnaspace.org